Persistent and chronic infections are maintained by a dynamic modulation of microbe - host cell interactions. During this process, microorganisms evolve and adapt to the host by regulating the expression of different genes, in particular those involved in virulence. At the bacterial population level, specific (possibly hypervirulent) clones may predominate at different times in individuals as well as groups of patients. The timely storage of microbial pathogens in the microbiology laboratory together with the availability of clinical data from the patients allows following virulence traits, host adaptation and changing epidemiology of the pathogens. Two specific examples are summarized below: 1) Work on Mycobacterium abscessus revealed high relatedness between strains involved in global outbreaks in cystic fibrosis patients. Outbreak strains undergo adaptative changes potentially towards more virulent and/or transmissible populations. Interestingly, M. abscessus virulence and adaptative features share striking similarities to those in Mycobacterium tuberculosis. 2) We have recently described a novel and emerging species of molds causing disease in immunocompromised patients. One example is the isolation of a novel species of Phellinus from a patient with chronic granulomatous disease. Review of clinical charts and laboratory data unveiled additional cases of this species and related species within the genus. Another example is the recovery of a recently described species of Mucor spp from several immunocompromised patients. Whole genome sequencing and comparative genomics of invasive and non invasive Mucor strains is underway.